Splinter Cell
by Baronvonblack
Summary: After a heated argument, Misato thought she would never see Shinji again. 2 years later, he returns, but he's now a different person.


A/N: I wanted to get this one off my chest. Timeline of events and actual events may not match the EVA timeline. Angel attacks have been drastically dragged apart.

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**2 years ago**

Shinji sat in the bathroom, tears streaming down his face. His whole body trembled violently, and he couldn't stop it.

There was a knock on the door.

"Go away!" Shinji sobbed. "Just…just leave me."

"Shinji?" Misato asked softly on the other side. "It's Misato. Are…are you alright?"

"I…I'm fine. Just wait, I'll be out in an hour."

"That's bull and you know it, Shinji. What's the problem?"

Shinji sighed as he fell apart. "I just killed my best friend…how…how would you feel?"

Misato sank to the ground on the other side. "It wasn't your fault. Your father did order you to…"

"Don't talk about my father…please, just don't talk about him."

The lady nodded in understanding. After what his dad had done to him, it was meant to happen anytime.

"I can't do it anymore, Misato," Shinji wept. "I can't pilot Eva."

"You have to be strong, Shinji. You mustn't run away."

"But now every time I get into it…I always see Toji's face. There's always…blood on my hands."

"Toji wouldn't have wanted to see you like this. You have to be strong, please!"

"You're not getting me!" Shinji yelled, finally losing it. "I cannot, and will not pilot EVA!"

"And why is that, pilot?" Misato shouted, standing up. "Because your friend died? You saved this city many times over, several thousand lives. How can one compare to several thousand?"

"You haven't been in that entry plug! You haven't felt everything that I've felt, but nothing compares to this! I KILLED another human!"

"This is war, soldier! People die, whether you like it or not!" Misato screamed. "Now get out and start dinner!"

Shinji fell silent within the bathroom, and Misato felt like she was being cruel, but he was the only one who could pilot Unit 01.

"I'm not doing it anymore," Shinji whispered. "I hate you."

Misato felt like he had thrust daggers into her. "What…did you say?"

The bathroom door opened. "I hate you," Shinji repeated. "I hate you, I hate you, I HATE YOU!"

With every passing moment he had been stepping forward, and Misato had been stepping back in obvious fear. This was a Shinji Ikari that fought in the Evangelions; this was Shinji Ikari, the soldier, the warrior.

"I hate you, and Asuka, and my father!" Shinji yelled. "I'm done here!" With that he stormed off to his room.

"What are you doing?" Misato shrieked.

Shinji came out with a bulky bag. "Packing!" He grabbed his ID card from his pocket, slapping it onto the ground. "Here! That's my formal resignation!"

"Where the hell do you have to go? There's nothing for you out there! This is your home!"

"Home is away from here!" Shinji snapped, walking past her.

"Shinji don't be so selfish!" Misato yelled, grabbing his wrist.

"Let go of me!" the pilot cried, wrestling with her as he struggled to get out of his grip.

"Stop it, Shinji! I said, STOP!"

SLAP!!

Misato looked horrified as she realised what she had just done.

Fresh tears were in his eyes as Shinji caressed the red mark on his cheek. "I knew…I knew I don't belong here…"

There was an awkward, tense silence as Shinji shouldered the large bag, walking to the doorway. "Goodbye, Misato…"

"NO WAIT!" Too late, he had shut the door.

Finally, Misato broke down and cried.

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Shinji sat on the bench at the train station two hours later, listening to his SDAT as he tried to forget everything.

A man sat beside him. "Hey, Shinji."

Shinji turned around to stare at the hooded man in surprise. He thought he was completely alone…

"Who are you?" the teen quickly blurted out.

"Me? Sam…Sam Fisher."

"You're not Japanese," Shinji stated, recognizing the heavy, throaty American accent.

"No, I'm not. American."

"Thought so," Shinji sighed.

"We've been watching your father for a long time, Shinji."

"I don't have a father…at least, not anymore." The teen snapped.

"He's done a lot of bad things in his life. But I'll be straight with you. Something's coming up that could endanger everyone…your friends, your people, the entire world."

"We already know about the Angels."

"Angels aren't our worst enemy. Our worst enemy is human, and you know who he is."

Shinji realised. "Gendo Ikari."

"He's going to do some horrible things, and only you can tell us, Shinji."

"I'm just a pilot," Shinji stated. "I don't know anything."

"…I see." Sam turned around. "Will? We're wasting our time, the kid doesn't know anything. Pick me up at the planned point."

Sam stood up. "Well, see ya around, kid."

Shinji sat rigid before standing up also. "Wait!"

Sam turned around. "What is it?" he asked gruffly.

"You said the Commander was going to do some horrible things," Shinji stated. "Things that would hurt all mankind."

"That's right. But it's not for you to know." With that Sam turned back and began to walk.

"Wait!"

This time when Sam turned back around all humour was lost. "Look kid, you don't have anything I want or need. Now just get on the train when it comes and continue on with the rest of your life. Forget about all this, forget we ever talked as well."

"I can't," Shinji stated, "Because YOU have something I want and need."

Sam raised an eyebrow. "And what is that?"

"I want to help you," Shinji said. "I want to do whatever I can to hurt NERV in any way."

"You know, for someone everyone calls a spineless wimp you sure have a lot of guts," Sam said, impressed. "But why should I accept this?"

"I'm tired of being a coward, of fighting for something I don't even believe in," Shinji said. "Of being weak, of being expendable. I want to come with you."

"Well that's all fine and dandy, but what I do is a dangerous business. If you're coming along you may, no definitely get hurt."

"I have nothing here with me now," Shinji said, a new demeanor rising in him. He HAD to have this. "I'll do anything."

Sam considered this. The boy seemed determined, and he could see that he wanted this more than anything. _Fine, might as well give him a shot. _"Will. Cancel that; pick us up at our current location. We have an extra passenger."

"Thank you," Shinji bowed. "You don't know how much this means to me."

"I hacked into the bugs those NERV agents put on your apartment – I heard your fight. If you do well, you may find what you want here." Sam said with a smirk.

A large dark van pulled up on the other side of the road.

Sam turned round. "That's our ride. So you coming?"

Shinji followed him as they got in the back.

"Will," Sam acknowledged as he got in the back.

"So who's this?" the field runner asked.

Sam grinned. "William, you're looking at the newest Splinter Cell."

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Almost a minute after they had left, a blue sports car raced to the train station, pulling up as the driver got out, sprinting to the moving train as it just left.

"SHINJI!"

Misato fell onto her knees, crying unstoppably. _Shinji…I'm so sorry…for everything…_

She stood up to see an abandoned SDAT lying on the bench.

Misato frowned as she picked it up. _Shinji would never leave this…so…why? What made him leave it?_

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Present day 

"I don't believe this…" Misato looked at the incoming train. "Why would he ever come back?"

After Shinji had left, the reactions from his associates had been mixed. Ritsuko completely understood, knowing the stress from piloting the Evangelions could be overbearing, so therefore killing one of his friends could have pushed him over the edge.

Asuka's reaction was predictable – she simply shrugged it off, labeling Shinji a coward and sissy for pulling out like this.

Gendo never batted an eye when she told him, the bridge bunnies also expected this to happen and for Rei…well no one knew what she thought.

So why, why would Shinji come back? What does he have to accomplish in coming here?

Angel attacks had slowed considerably – the last one they had was the 14th and that was last year.

Onboard the train, a young man looked out the window to see a familiar blue sports car with his former guardian beside it. He sighed, leaning back in his chair as the train came to a full stop.

Outside, Misato watched as the train halted. She took in a deep breath.

A lone man came out of the train – no one really came here now with the Angels, even if they had been given a long break. He was wearing black cargo pants and a brown jacket with dark sunglasses that hid his eyes.

Misato couldn't believe this was Shinji – he was at least now as tall as her! "…Shinji?"

The man walked up to her, slipping off his sunglasses to reveal his familiar blue eyes. "Misato."

Immediately Misato jumped on him, hugging him tightly. "Oh, Shinji! I missed you so much!"

Shinji's fighting instincts screamed at him to throw her off, but the former pilot silenced them through his hardened disciplined as he quickly forced a smile. "I missed you too."

"Come on! I'll drive you back to the apartment, everybody's over there!"

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Shinji watched the familiar buildings fly past as the car flew recklessly along the road.

Misato quickly noticed this. _He's not bothered by my driving… _"So Shinji, what have you been doing while away?"

"Oh, you know, I've been around…"

"Come on…" Misato leaned forward slightly. "Been with a few girls, right?"

Shinji laughed. "Only one or two…"

_WHAT? _Misato turned the wheel suddenly, the tires screaming as the car spun right around. "You're not my Shinji! What have you done with my Shinji?"

"He's right here," Shinji replied, hand halfway up to reach his holstered pistol inside his jacket. "People change, Misato."

Misato slowed down considerably as they got to the apartment building. "I know…it's just the old Shinji would have been embarrassed by this."

Shinji remembered his training. "Some things along the way have changed me, Misato. Don't worry though, I'm still Shinji."

He quickly changed the subject. "So, how is my old man? Still in charge of NERV?"

The Major missed the sarcastic tone in his voice. "Yep, although it's been pretty quiet. Not very many Angels have attacked now."

"I see. Well at least that's a relief."

"Will he come to see me?"

"You know your dad, definitely not unless you came back to pilot EVA."

"Any renovations to the geo-front?"

"Nope, it's the same as when you left it."

Shinji smirked. "That's good…"

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A/N: Numerous flashbacks will piece together the 2 years, but for now this is the first chapter.


End file.
